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Title: Assessment of genome integrity in cattle transgenic cell lines using array CGH

Author
item Liu, Ge - George
item HOU, YALI - University Of Maryland
item ROBL, JAMES - Hematech, Inc
item KUROIWA, YOSHI - Hematech, Inc
item WANG, ZHONGDE - Hematech, Inc

Submitted to: Genome Integrity
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/9/2011
Publication Date: 5/23/2011
Citation: Liu, G., Hou, Y., Robl, J.M., Kuroiwa, Y., Wang, Z. 2011. Assessment of genome integrity in cattle transgenic cell lines using array CGH. Genome Integrity. 2(1):6-10.

Interpretive Summary: In this study, we successfully implemented array Comparative Genomic Hybridization (CGH) as a genome-wide tool to systematically exam the genome integrity. We tested 9 cell lines showing differential efficiencies during animal cloning) Our plan included the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines with either high or low cloning efficiencies. We detected similar amounts of differences between the control hybridizations and the comparative analyses of both “high” and “low” cell lines. It is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). In summary, these findings reveal that during animal cloning, genomes remain essentially intact i.e. free of large scale genomic structural variations, pinpointing to the importance of other causes like epigenetic changes.

Technical Abstract: Transgenic cattle carrying multiple genomic modifications have been produced by serial rounds of somatic cell chromatin transfer (cloning) of sequentially genetically targeted somatic cells. However, cloning efficiency tends to decline with the increase of rounds of cloning. It is possible that multiple rounds of cloning compromise the genome integrity or introduce epigenetic errors in the resulting cell lines, rendering cloning efficiency decline. To test these possibilities, we performed 9 high density array Comparative Genomic Hybridization (CGH) experiments to test the genome integrity in 3 independent bovine transgenic cell lineages generated from genetic modification and cloning. Our plan included the control hybridizations (self to self) of the 3 founder cell lines and 6 comparative hybridizations between these founders and their derived cell lines with either high or low cloning efficiencies. We detected similar amounts of differences between the control hybridizations (6, 9 and 41 differences) and the comparative analyses of both “high” and “low” cell lines (ranging from 4 to 45 with a mean of ~16). Since almost half of these differences shared the same type (loss or gain) and were located in nearby genomics regions, it is likely that they were not true differences but caused by systematic factors associated with local genomic features (e.g. GC contents). In summary, these findings reveal that large genomic structural variations are less likely to arise during genetic targeting and serial rounds of cloning, fortifying the notion that epigenetic errors introduced from serial cloning are responsible for the cloning efficiency decline.